how should I put in the program so that it will reset the count whenever the the ref_pos_b and ref_pos_e is different from the proceeding lines.

Just reset it if the current value isn't equal to the previous one, e.g.

   if ($ref_pos_b eq $pre_ref_pos_b) {
       $count++;
   } else {
       $count = 1;  # reset
   }
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